Microbial coalbed gas (CBG) and shale gas (SG), predominately composed of methane (CH4) and carbon dioxide (CO2), are important economic resources and potent greenhouse gases. Although isotopic equilibrium of CH4 and CO2 has been observed in microbial CBG and SG basins, it is difficult to judge under what geological conditions equilibrium is achieved. Moreover, the effects of CO2 dissolution on the isotopic fractionation process need to be considered. We use data from eight microbial CBG and SG basins to discuss the geological conditions in which equilibrium and kinetic isotopic fractionation in CH4-CO2-HCO3− system is achieved. Based on isotopic equilibrium temperatures calculated using computer codes developed in MatLab software, we show that, in deep and closed reservoirs, the CH4-CO2 and CH4-HCO3− are close to carbon isotope equilibrium. In contrast, in shallow and open reservoirs, they are in disequilibrium. The CO2-HCO3− is in disequilibrium in most reservoirs. We propose that both low free energy gradients and long coexisting time of CH4 and CO2/HCO3− are necessary to attain isotopic equilibrium. However, it is difficult to accurately estimate the timescale for attaining isotope equilibrium among them. In general, a closed and deep CBG/SG reservoir is likely to be geologically and geochemically stable over long timescales, favoring isotopic equilibrium of CH4-CO2 and CH4-HCO3−. However, a shallow and open reservoir is unfavourable for their isotopic equilibrium due to shorter timescales for the coexistence of CH4-CO2-HCO3−. Using data from systems close to equilibrium, we estimated the percentage of CO2 in total CH4 and CO2 in CBG reservoirs in various basins to be from 27% to 50%, where methanogenesis is mainly by CO2 reduction. This is significantly higher than the CO2 content (1% to 15%) in gaseous CH4 and CO2 in these basins but is consistent with those (36% to 48%) from culture experiments for coal conversion by methanogenesis. Further study shows that 53–99% of the CO2 formed during CBG generation has dissolved into groundwaters to form dissolved inorganic carbon (DIC) in CBG reservoirs. We propose that CO2 dissolution likely has significantly affect the abundance and isotopic compositions of gaseous CO2 in subsurface.